\HeaderA{runAlignment}{A function to establish preliminaries for the
compBijection function.}{runAlignment}
\keyword{array}{runAlignment}
\keyword{datagen}{runAlignment}
\begin{Description}\relax
This function creates the record keeping bijMat and calls the
\code{\LinkA{compBijection}{compBijection}} function.
\end{Description}
\begin{Usage}
\begin{verbatim}
runAlignment(TSNMat, estMat, c2kMat)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{TSNMat}] The first bipartite graph matrix
\item[\code{estMat}] The second bipartite graph matrix
\item[\code{c2kMat}] The matrix of similarity index between TSNMat and estMat
\end{ldescription}
\end{Arguments}
\begin{Value}
The matrix bijMat with an alignment calculated by the function
\code{\LinkA{compBijection}{compBijection}}
\end{Value}
\begin{Author}\relax
Tony Chiang
\end{Author}
\begin{Examples}
\begin{ExampleCode}
#go = getGOInfo()
#mips = getMipsInfo()
#goM = createGOMatrix(go)
#mipsM = createMipsMatrix(mips)
#cc = runCompareComplex(mipsM, goM, byWhich = "ROW")
#align = runAlignment(mipsM, goM, cc$simInd)
\end{ExampleCode}
\end{Examples}

